Whole-genome sequence and assembly of the Java']Javan gibbon (Hylobates moloch)

被引：3

作者：

Escalona, Merly ^{[1
]}

VanCampen, Jake ^{[2
]}

Maurer, Nicholas W. ^{[1
]}

Haukness, Marina ^{[1
,3
]}

Okhovat, Mariam ^{[2
]}

Harris, Robert S. ^{[4
]}

Watwood, Allison ^{[4
]}

Hartley, Gabrielle A. ^{[5
,6
]}

O'Neill, Rachel J. ^{[5
,6
]}

Medvedev, Paul ^{[7
,8
,9
,10
]}

Makova, Kateryna D. ^{[4
,7
,8
]}

Vollmers, Christopher ^{[1
]}

Carbone, Lucia ^{[2
,11
,12
,13
]}

Green, Richard E. ^{[1
]}

机构：

[1] Univ Calif Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA

[2] Oregon Hlth & Sci Univ, Dept Med, Knight Cardiovasc Inst, Portland, OR 97239 USA

[3] Univ Calif Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA

[4] Penn State Univ, Dept Biol, University Pk, PA 16802 USA

[5] Univ Connecticut, Dept Mol & Cell Biol, Storrs, CT 06296 USA

[6] Univ Connecticut, Inst Syst Genom, Storrs, CT 06296 USA

[7] Penn State Univ, Ctr Med Genom, University Pk, PA 16802 USA

[8] Penn State Univ, Ctr Computat Biol & Bioinformat, University Pk, PA 16802 USA

[9] Penn State Univ, Dept Comp Sci & Engn, University Pk, PA 16802 USA

[10] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA

[11] Oregon Hlth & Sci Univ, Dept Mol & Med Genet, Portland, OR 97239 USA

[12] Oregon Natl Primate Res Ctr, Div Genet, Beaverton, OR 97006 USA

[13] Oregon Hlth & Sci Univ, Dept Informat & Clin Epidemiol, Portland, OR 97239 USA

来源：

JOURNAL OF HEREDITY | 2023年 / 114卷 / 01期

基金：

美国国家科学基金会;

关键词：

genome assembly; gibbon; Hi-C; long reads; proximity ligation; KARYOTYPE; DISCOVERY; FRAMEWORK; ALIGNMENT; EVOLUTION; CONCOLOR; FORMAT; TOOL; LAR;

D O I：

10.1093/jhered/esac043

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.

引用

页码：35 / 43

页数：9

共 48 条

[1] Cooler: scalable storage for Hi-C data and other genomically labeled arrays
Abdennur, Nezar
Mirny, Leonid A.
[J]. BIOINFORMATICS, 2020, 36 (01) : 311 - 316
[2] Genetic variability in mtDNA of the silvery gibbon: Implications for the conservation of a critically endangered species
Andayani, N
Morales, JC
Forstner, MRJ
Supriatna, J
Melnick, DJ
[J]. CONSERVATION BIOLOGY, 2001, 15 (03) : 770 - 775
[3] Audebert JB., 1798, HIST NATURELLE SINGE
[4] Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
Boeva, Valentina
Popova, Tatiana
Bleakley, Kevin
Chiche, Pierre
Cappo, Julie
Schleiermacher, Gudrun
Janoueix-Lerosey, Isabelle
Delattre, Olivier
Barillot, Emmanuel
[J]. BIOINFORMATICS, 2012, 28 (03) : 423 - 425
[5] D-GENIES: dot plot large genomes in an interactive, efficient and simple way
Cabanettes, Floreal
Klopp, Christophe
[J]. PEERJ, 2018, 6
[6] A high-resolution map of synteny disruptions in gibbon and human genomes
Carbone, Lucia
Vessere, Gery M.
ten Hallers, Boudewijn F. H.
Zhu, Baoli
Osoegawa, Kazutoyo
Mootnick, Alan
Kofler, Andrea
Wienberg, Johannes
Rogers, Jane
Humphray, Sean
Scott, Carol
Harris, R. Alan
Milosavljevic, Aleksandar
de Jong, Pieter J.
[J]. PLOS GENETICS, 2006, 2 (12): : 2162 - 2175
[7] Gibbon genome and the fast karyotype evolution of small apes
Carbone, Lucia
Harris, R. Alan
Gnerre, Sante
Veeramah, Krishna R.
Lorente-Galdos, Belen
Huddleston, John
Meyer, Thomas J.
Herrero, Javier
Roos, Christian
Aken, Bronwen
Anaclerio, Fabio
Archidiacono, Nicoletta
Baker, Carl
Barre, Daniel
Batzer, Marka.
Beal, Kathryn
Blancher, Antoine
Bohrson, Craig L.
Brameier, Markus
Campbell, Michael S.
Capozzi, Oronzo
Casola, Claudio
Chiatante, Giorgia
Cree, Andrew
Damert, Annette
de Jong, Pieter J.
Dumas, Laura
Fernandez-Callejo, Marcos
Flicek, Paul
Fuchs, Nina V.
Gue, Ivo
Gut, Marta
Hahn, Matthew W.
Hernandez-Rodriguez, Jessica
Hillier, LaDeana W.
Hubley, Robert
Ianc, Bianca
Izsvak, Zsuzsanna
Jablonski, Nina G.
Johnstone, Laurel M.
Karimpour-Fard, Anis
Konkel, Miriam K.
Kostka, Dennis
Lazar, Nathan H.
Lee, Sandra L.
Lewis, Lora R.
Liu, Yue
Locke, Devin P.
Mallick, Swapan
Mendez, Fernando L.
[J]. NATURE, 2014, 513 (7517) : 195 - +
[8] Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons
Carbone, Lucia
Harris, R. Alan
Mootnick, Alan R.
Milosavljevic, Aleksandar
Martin, David I. K.
Rocchi, Mariano
Capozzi, Oronzo
Archidiacono, Nicoletta
Konkel, Miriam K.
Walker, Jerilyn A.
Batzer, Mark A.
de Jong, Pieter J.
[J]. GENOME BIOLOGY AND EVOLUTION, 2012, 4 (07): : 760 - 770
[9] Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution
Carbone, Lucia
Harris, R. Alan
Vessere, Gery M.
Mootnick, Alan R.
Humphray, Sean
Rogers, Jane
Kim, Sung K.
Wall, Jeffrey D.
Martin, David
Jurka, Jerzy
Milosavljevic, Aleksandar
de Jong, Pieter J.
[J]. PLOS GENETICS, 2009, 5 (06):
[10] The variant call format and VCFtools
Danecek, Petr
Auton, Adam
Abecasis, Goncalo
Albers, Cornelis A.
Banks, Eric
DePristo, Mark A.
Handsaker, Robert E.
Lunter, Gerton
Marth, Gabor T.
Sherry, Stephen T.
McVean, Gilean
Durbin, Richard
[J]. BIOINFORMATICS, 2011, 27 (15) : 2156 - 2158

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